1 answer

What we have been thinking about is having the ability to put multiple BAM sources into a single plot (possibly coloring by source to see their relative contributions). That would give you an aggregate read-depth (not an average). Because you are visualizing discrete reads in both the pile-up and coverage view (in the sense the coverage counts the number of missenses/insertions/deletions), averages are a hard thing to visualize without creating a completely different plot type.

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